Unique Name	Descriptor	Wide Peak Limits	Peak Limits	Region Limits	q values	Residual q values after removing segments shared with higher peaks	Broad or Focal	Amplitude Threshold	TCGA-FF-8041-01A-11D-2209-01	TCGA-FF-8042-01A-11D-2209-01	TCGA-FF-8043-01A-11D-2209-01	TCGA-FF-8046-01A-11D-2209-01	TCGA-FF-8047-01A-11D-2209-01	TCGA-FF-8061-01A-11D-2209-01	TCGA-FF-8062-01A-11D-2209-01	TCGA-FM-8000-01A-11D-2209-01	TCGA-G8-6324-01A-11D-2209-01	TCGA-G8-6325-01A-11D-2209-01	TCGA-G8-6326-01A-11D-2209-01	TCGA-G8-6906-01A-11D-2209-01	TCGA-G8-6907-01A-11D-2209-01	TCGA-G8-6909-01A-11D-2209-01	TCGA-G8-6914-01A-11D-2209-01	TCGA-GR-7351-01A-11D-2209-01	TCGA-GR-7353-01A-11D-2209-01	
Amplification Peak 1	2p16.1	chr2:60700794-61776974(probes 164614:165135)	chr2:60702767-61776901(probes 164615:165134)	chr2:58198363-63389210(probes 162957:165892)	1.6001e-07	 1.6001e-07		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	1	0	2	0	0	2	0	2	0	0	0	0	1	2	0	0	0	
Deletion Peak  1	1p22.1  	chr1:86114902-119946150(probes 47388:67447)      	chr1:93640821-93753734(probes 51936:51976)          	chr1:93683544-93688818(probes 51957:51958)          	0.14326	  0.14326		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	
Deletion Peak  2	1q43    	chr1:15569713-249250621(probes 6737:129201)      	chr1:241292293-245031806(probes 125743:127985)    	chr1:240756850-245386854(probes 125377:128157)    	0.14326	  0.14326		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	
Deletion Peak  3	2q22.3  	chr2:115916647-168118431(probes 189684:217729)  	chr2:145267653-150446366(probes 204762:207403)    	chr2:140592849-151019952(probes 201921:207829)    	0.14326	  0.14326		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	1	0	1	0	0	0	1	0	0	0	0	0	0	1	0	
Deletion Peak  4	6q14.1  	chr6:74403249-119259018(probes 610912:635871)    	chr6:79642076-79792746(probes 613815:613874)        	chr6:79719282-79724242(probes 613845:613846)        	0.15232	  0.21831		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	1	0	1	0	0	0	0	0	1	0	1	0	0	0	0	0	
Deletion Peak  5	6q23.3  	chr6:137814087-138410514(probes 647392:647786)  	chr6:138182417-138214040(probes 647665:647675)    	chr6:138159537-138215573(probes 647653:647677)    	0.14326	  0.14326		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	0	0	1	0	1	0	1	0	0	0	
Deletion Peak  6	8q12.1  	chr8:42706321-71525707(probes 772927:786695)      	chr8:59713200-60034328(probes 779840:780074)        	chr8:59869733-59872874(probes 779958:779959)        	0.24056	  0.24056		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	
Deletion Peak  7	9p21.3  	chr9:21555227-22448737(probes 843091:843621)      	chr9:21959052-21997722(probes 843308:843321)        	chr9:21846441-22546329(probes 843250:843658)        	0.048548	 0.048548		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	1	0	0	1	0	0	0	0	1	0	1	0	0	0	0	0	
Deletion Peak  8	10q23.31	chr10:83636583-115949820(probes 946176:966341)  	chr10:89617402-89735596(probes 950080:950267)      	chr10:89665540-89725856(probes 950147:950251)      	0.14326	  0.14326		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	
Deletion Peak  9	13q33.3 	chr13:26781529-115169878(probes 1133840:1186722)	chr13:107820390-108522799(probes 1182252:1182871)	chr13:101863055-115169878(probes 1178144:1186722)	0.14326	  0.14326		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	
Deletion Peak 10	15q15.1 	chr15:40395404-45299932(probes 1244550:1246643)  	chr15:42129513-42186481(probes 1245340:1245353)    	chr15:42160944-42166137(probes 1245347:1245348)    	0.14326	  0.14326		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	1	1	
Deletion Peak 11	16p13.13	chr16:4560058-20812500(probes 1282092:1289985)    	chr16:10970628-11020236(probes 1286213:1286259)    	chr16:11000849-11004362(probes 1286237:1286238)    	0.24056	  0.24056		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	1	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	
Deletion Peak 12	17q24.1 	chr17:1-81195210(probes 1321560:1358563)           	chr17:63003700-63057650(probes 1349249:1349282)    	chr17:62984378-63140426(probes 1349238:1349321)    	0.24086	  0.24056		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	
Amplification Peak 1 - CN values	2p16.1	chr2:60700794-61776974(probes 164614:165135)	chr2:60702767-61776901(probes 164615:165134)	chr2:58198363-63389210(probes 162957:165892)	1.6001e-07	 1.6001e-07		Actual Copy Change Given	0.37446	0.023005	3.6569	0.0114	-0.0068072	0.91319	0.0035108	2.7335	-0.0067813	-0.0013239	0.011121	0.0033299	0.74727	1.9622	0.010006	0.033408	0.0015255	
Deletion Peak  1 - CN values	1p22.1  	chr1:86114902-119946150(probes 47388:67447)      	chr1:93640821-93753734(probes 51936:51976)          	chr1:93683544-93688818(probes 51957:51958)          	0.14326	  0.14326		Actual Copy Change Given	-0.018765	-0.011795	0.0041629	-0.0011087	0.0036076	0.0093098	-0.0086687	0.0033299	0.0016642	-0.26547	0.00027728	-0.015329	0	-0.00055444	-0.00069303	0.0054139	-0.6401	
Deletion Peak  2 - CN values	1q43    	chr1:15569713-249250621(probes 6737:129201)      	chr1:241292293-245031806(probes 125743:127985)    	chr1:240756850-245386854(probes 125377:128157)    	0.14326	  0.14326		Actual Copy Change Given	-0.03783	-0.7911	-0.89213	-0.0086614	-0.92904	-0.046177	0.0024001	0.74271	0.0016642	-0.0061319	0.00027728	-0.010922	0	-0.00041585	-0.012438	-0.0035449	0.57849	
Deletion Peak  3 - CN values	2q22.3  	chr2:115916647-168118431(probes 189684:217729)  	chr2:145267653-150446366(probes 204762:207403)    	chr2:140592849-151019952(probes 201921:207829)    	0.14326	  0.14326		Actual Copy Change Given	0.37263	-0.014228	-0.8541	-0.0022168	-0.88588	0.022198	0.0035108	0.0066653	-0.33941	-0.0013239	0.00013863	0.0033299	-0.0055914	-0.0049844	0.0028189	-0.53144	0.0029133	
Deletion Peak  4 - CN values	6q14.1  	chr6:74403249-119259018(probes 610912:635871)    	chr6:79642076-79792746(probes 613815:613874)        	chr6:79719282-79724242(probes 613845:613846)        	0.15232	  0.21831		Actual Copy Change Given	-0.0096806	-0.77905	0.012581	-0.54179	0.029325	-0.04356	-0.012616	0.0024969	0.0020805	-0.28139	-0.0021819	-0.77277	0.0040243	0.015866	0	0.0030562	-0.0022168	
Deletion Peak  5 - CN values	6q23.3  	chr6:137814087-138410514(probes 647392:647786)  	chr6:138182417-138214040(probes 647665:647675)    	chr6:138159537-138215573(probes 647653:647677)    	0.14326	  0.14326		Actual Copy Change Given	-0.0096806	0.71565	0.012581	0.0080567	0.022444	-0.010784	0.014233	0.0024969	0.0020805	-0.28139	-0.0021819	-1.2929	0.0033299	-1.0477	0.010567	0.0030562	-0.0022168	
Deletion Peak  6 - CN values	8q12.1  	chr8:42706321-71525707(probes 772927:786695)      	chr8:59713200-60034328(probes 779840:780074)        	chr8:59869733-59872874(probes 779958:779959)        	0.24056	  0.24056		Actual Copy Change Given	0.38237	-0.0087146	-0.091836	-0.0040162	-0.91485	0.016425	0.0043442	-0.0048461	0.0072217	0.0039474	-0.010784	0.057653	0.001803	-0.010508	-0.0054461	-0.0019888	-0.66615	
Deletion Peak  7 - CN values	9p21.3  	chr9:21555227-22448737(probes 843091:843621)      	chr9:21959052-21997722(probes 843308:843321)        	chr9:21846441-22546329(probes 843250:843658)        	0.048548	 0.048548		Actual Copy Change Given	0.4996	-1.2929	-0.0029299	-0.0069195	-1.2929	-0.020319	-0.0026172	-0.005261	0.0063871	-0.2765	-0.0030475	-0.73906	0.0038854	-0.0027707	-0.0053992	-0.0060177	0.0055529	
Deletion Peak  8 - CN values	10q23.31	chr10:83636583-115949820(probes 946176:966341)  	chr10:89617402-89735596(probes 950080:950267)      	chr10:89665540-89725856(probes 950147:950251)      	0.14326	  0.14326		Actual Copy Change Given	0.10521	-0.013781	-0.0025146	-0.0081624	-0.0030336	0.0020805	-0.0083968	-0.0036011	0	0.0022813	-0.0015243	-0.0038779	-0.63235	0	-0.013265	-0.006505	-1.0234	
Deletion Peak  9 - CN values	13q33.3 	chr13:26781529-115169878(probes 1133840:1186722)	chr13:107820390-108522799(probes 1182252:1182871)	chr13:101863055-115169878(probes 1178144:1186722)	0.14326	  0.14326		Actual Copy Change Given	-0.025893	-0.82252	-0.87565	0.46844	0.012237	-0.079476	-0.0010668	0.00055459	-0.00052854	-0.0022935	-0.007472	0.01959	0.011171	0.003191	-0.011611	-0.57851	-0.014699	
Deletion Peak 10 - CN values	15q15.1 	chr15:40395404-45299932(probes 1244550:1246643)  	chr15:42129513-42186481(probes 1245340:1245353)    	chr15:42160944-42166137(probes 1245347:1245348)    	0.14326	  0.14326		Actual Copy Change Given	-0.020138	-0.0037395	-0.841	0.48251	-0.011266	-0.0036011	0.0054559	-0.015466	-0.0038779	0.0042253	0.0013868	-0.012576	-0.84267	0.44664	0.019643	-0.54451	-0.63585	
Deletion Peak 11 - CN values	16p13.13	chr16:4560058-20812500(probes 1282092:1289985)    	chr16:10970628-11020236(probes 1286213:1286259)    	chr16:11000849-11004362(probes 1286237:1286238)    	0.24056	  0.24056		Actual Copy Change Given	-0.94276	0.013492	-0.91696	-0.0091286	0.0048579	-0.0031859	-0.00995	-0.86798	-0.0087146	0.00131	0.0057313	-0.034223	0.001803	0.031718	0.0094365	0.0013868	0.01308	
Deletion Peak 12 - CN values	17q24.1 	chr17:1-81195210(probes 1321560:1358563)           	chr17:63003700-63057650(probes 1349249:1349282)    	chr17:62984378-63140426(probes 1349238:1349321)    	0.24086	  0.24056		Actual Copy Change Given	0.37726	0.020623	-0.0097013	-0.0070576	-0.024798	-0.0016629	0.0036497	-1.2929	-0.01284	-0.0058905	-0.00018913	-0.03054	-0.86578	-0.02151	0.017124	-0.011749	0.020343	
